Conservation Genetics

Data Analysis Course - 9-14 September - Porto - Portugal

Recent Approaches for Estimation of Population Size, Structure, Gene flow and Selection Detection

List of Instructors

The following instructors are confirmed: 
Fred Allendorf
Mark Beaumont
Albano Beja-Pereira
Pierre Faubet
Oscar Gaggiotti
Gilles Guillot
Gordon Luikart
Christian Schlötterer
Mike Schwartz
David Tallmon
Miguel Angel Toro
Robin Waples

Instructors' biographies

Fred Allendorf

Research Interests: Fred's research interests are in the areas of evolution, population genetics, and conservation biology. The primary current focus of his research is the application of genetics to the conservation of animals and plants. We in the Montana Conservation Genetics Laboratory are active in applying the principles of population and evolutionary genetics to the conservation of salmonid fishes and a variety of other species. We are using molecular genetics to describe intraspecific patterns of genetic variation and phylogenetic relationships in many of these species. In addition, we are developing the theory and statistical analysis needed to apply the principles of population genetics to conservation problems. We have written a conservation genetics book (Conservation and the genetics of populations) which has recently been published by Blackwell.

Example publications:
Allendorf, F.W., P.R. England, G. Luikart, P.A. Ritchie, and N. Ryman. In press. Genetic effects of harvest on wild animal populations. Trends in Ecol. Evol.
Allendorf, F.W., and G. Luikart. 2007. Conservation and the Genetics of Populations. Blackwell Publishing.
Palsbøll, P.J., Bérubé, M., and F. W. Allendorf. 2007. Defining management units among natural populations from genetic markers. Trends in Ecol. Evol. 22:11-16.
Haig, S.M., and F.W. Allendorf. 2006. Hybrids and policy. In: The Endangered Species Act at Thirty: Conserving Biodiversity in Human-Dominated Landscapes, Vol. 2. J.M. Scott, D.D. Goble, and F. Davis, editors. Island Press. pp. 150-163.
Funk, W.C., A.E. Greene, P.S. Corn, and F.W. Allendorf. 2005. High dispersal in a frog suggests that it is vulnerable to habitat fragmentation. Biology Letters 1:13-16.

Mark Beaumont

Mark Beaumont is a NERC Advanced Fellow at the University of Reading in England. He was a conservation genetics fellow at the Institute of Zoology and a Wellcome Research Fellow in Mathematical Biology at Queen Mary and Westfield College. He has over 50 publications and has been on the review board of Heredity and other journals. He has projects in the following research areas:
  1. Bayesian methods for quantifying levels of adaptive divergence between populations using gene frequency data,
  2. The influence of propagule banks on demography and genetic diversity in freshwater invertebrates and plants,
  3. Development of statistical methods to infer gene flow from crop plants into wild relatives, and
  4. Development of statistical tools to infer demographic history using linked microsatellite markers.

Homepage.

Albano Beja-Pereira

Albano Beja-Pereira is a Research Fellow with the Portuguese Science Foundation at the Center for Investigation of Biodiversity and Genetic Resources (CIBIO) and the University of Porto in Portugal. His research focuses on the conservation genetics and evolutionary history of wild and domestic ungulates. Recent publications include

  1. Genetic evidence for multiple origins of European cattle in Near-East, Africa, and Europe,
  2. Gene-culture coevolution between cattle milk protein genes and human lactase gene,
  3. Twenty polymorphic microsatellites in two of the most threatened ungulates: Gazella dorcas and Ammotragus lervia (Bovidae, Artiodactlya), and
  4. Genetic characterization of Southwestern European Bovine Breeds.

Homepage.

Pierre Faubet

Perre Faubet is a PhD student at the Joseph Fourier University in Grenoble, France. He is also a member of Oscar Gaggiotti's team at the Laboratoire d'Ecologie Alpine. His research aims at developing models and statistical methods for the study of the spatial distribution of genetic diversity. More specifically his work focuses on the influence of environmental factors on gene flows and/or local adaptation. Recent publications include:
  1. A new Bayesian method to identify the environmental factors that influence recent migration.
  2. Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates.

Homepage.

Oscar Gaggiotti

Oscar Gaggiotti's is a professor at the University Joseph Fourier in Grenoble, France. He is also head of the Population Genomics and Biodiversity team of the Laboratoire d'Ecologie Alpine. His research focuses on developing theory and statistical methods aimed at bridging the gap between population ecology, population genetics and evolution. Much of his research is applied to the study of metapopulations. Recent publications include:
  1. Identifying the environmental factors that determine the genetic structure of Populations
  2. Ecology, genetics and evolution of metapopulations
  3. Patterns of colonization in a metapopulation of grey seals

Homepage

Gilles Guillot

Gilles Guillot holds a permanent position as a researcher at the Department of Applied Mathematics at INRA (Institut National de la Recherche Agronomique), in Paris, France. He is currently on a three-year leave from this position to work at the Centre for Ecological and Evolutionary Synthesis Department of Biology, University of Oslo.
His scientific areas of interest include Spatial statistics , Bayesian modeling , Computational statistics, R packages development , Population genetics and molecular ecology , Environmental statistics and Statistical analysis of microarray data .

Selected references:
G. Guillot, F. Santos and A. Estoup. Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics, 2008.
G. Guillot, M. Olsson, M. Benson, M. Rudemo. Discrimination and scoring using small sets of genes for two-sample microarray data. Mathematical Biosciences, 5(2), 195-203, 2007.
A. Coulon, Guillot G., Cosson J.-F., Angibault J.M.A., Aulagnier S. , Cargnelutti B., Galan M., Hewison A.J.M. Genetic structure is influenced by lansdcape features.
G. Guillot, Mortier, F., Estoup, A. Geneland : A program for landscape genetics. Molecular Ecology Notes, 5, 712-715, 2005.
G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280, 2005. See this URL.

Homepage.

Gordon Luikart

Gordon Luikart is a Research Professor in the Center for Investigation of Biodiversity and Genetic Resources at the University of Porto, Portugal, and a Research Associate Professor at the University of Montana. He was a Research Scientist with the Centre National de la Recherche Scientifique (CNRS) at the University Joseph Fourier in Grenoble, France. His research focuses on the conservation and genetics of wild and domestic animals. He is a member of the IUCN specialists group for Caprinae (mountain ungulate) conservation. With Fred Allendorf, he has written a conservation genetics book (Conservation and the genetics of populations) which has recently been published by Blackwell.

Recent publications include:
  1. Impacts of modern molecular techniques on conservation biology,
  2. Genetic rescue of an insular population of large mammals,
  3. Estimating effective population size from linkage disequilibrium: severe bias using small samples.
  4. Genetic effects of harvest on wild animal populations.

Homepage

Christian Schlötterer

Christian is a professor in the Institut für Tierzucht und Genetik at the Veterinärmedizinische Universität in Austria. His research uses powerful population genetics tools (including 454 sequencing) to identify genes under selection. His team conducts functional validation of ecologically important variants using new functional approaches suitable to measure effects that are important in the wild, but difficult to score in the laboratory. Innovation is a key component of evolution and it can be observed at all taxonomic levels. The adaptation of natural populations to their environment also provides a rich repertoire of functional innovations. We use a combined approach of functional genetics and statistical methods to identify and characterize intra- and inter-specific functional innovations.

Recent Publications:
  1. African Drosophila melanogaster and D. simulans populations have similar levels of sequence variability, suggesting comparable effective population sizes. Genetics. 2008 178:405-12.
  2. Drosophila unleashed: the 12-genome update of the genetic power horse has been released. Heredity. 2008 (4):337-8. Epub 2007 Dec 5. No abstract available. Erratum in: Heredity. 2008 100:440.
  3. Gene expression profiling by massively parallel sequencing. Genome Res. 2008 18:172-7.
  4. Variation in male courtship song traits in Drosophila virilis: the effects of selection and drift on song divergence at the intraspecific level. Behav Genet. 2008 38:82-92.
  5. Identification of selective sweeps using a dynamically adjusted number of linked microsatellites. Genetics. 2007 175:207-18.

Home page

Mike Schwartz

Is director of the wildlife genetics lab of the US Forest Service in Missoula, Montana. They conduct research that is integrated with USFS management needs across North America. The wildlife genetics laboratory also works with States, Tribes, Universities and private groups answering questions in wildlife genetics, and providing answers to pressing wildlife management needs. Recent publications include:
  1. Landscape genetics: combining landscape ecology and population genetics
  2. Hybridization between Canada lynx and bobcats: Genetic results and management implications
  3. Genetic monitoring of individuals, populations, and species in the Wild

Homepage.

David Tallmon

Dave Tallmon is an Assistant Professor at the University of Alaska, Juneau. His Research focuses upon understanding the dynamics of natural populations. He combines demographic models, molecular data, and field data to infer important parameters for single populations and metapopulations. He has used models based on likelihood and approximate Bayesian computation to infer demographic vital rates and effective population size. His work has application in conservation and evolutionary biology. Publications include the following:
  1. the alluring simplicity and complex reality of genetic rescue,
  2. effective population size estimation using approximate Bayesian computation, and
  3. Insights into vole populations from combined genetic and demographic data.

Homepage.

Miguel Angel Toro

Miguel A. Toro is a senior scientist at the Department of Animal Breeding in the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). He has been working on the genetic management of conservation programs of domestic species especially in pigs. Particular interests include:
  1. Using molecular markers to estimate coancestry
  2. Combining molecular and genealogical information for the genetic management of small populations
  3. Detecting the foot print of selection in the domestication process
  4. Criteria for prioritization breeds in conservation

Robin Waples

Robin Waples is a senior scientist at the Northwest Fisheries Science Center of the National Marine Fisheries Service in Seattle. Robin led the Conservation Biology Division for a decade conducting comprehensive reviews of the status of Pacific salmonids under the US federal Endangered Species Act. Particular interests include:
  1. adapting standard population genetics theory so that it can be applied to real-world problems;
  2. combining diverse types of information (molecular genetics; life history; ecology) to characterize hierarchical levels of diversity in Pacific salmon;
  3. assessing viability of complex conservation units that include multiple independent populations and diverse ecotypes;
  4. methods for analyzing gene flow and population structure.

Homepage.